September 16, 2008

Why I won't be testing with 23andMe (yet)

Since the announcement of the price reduction of the 23andMe service, I had a couple of readers e-mail me, asking whether I thought it was worth it. My response was to do their own research to figure out whether the information they would learn would be worth the asking price.

The frivolous kind is perhaps a good and safe topic for conversation (as opposed, e.g., to Schizophrenia) but its value is obviously not $400.

The obvious kind tells you something that you already know about yourself; it only confirms that you have the genes for your known phenotype. Again, this is not useful information, unless perhaps your spouse orders a test too: then, you could sometimes calculate the chances of your children presenting a phenotype for simple quasi-Mendelian traits.

The medical kind is potentially useful. It is for this kind of information that you should research the traits on offer, to see if (i) they interest you, and (ii) there are strong associations for them. The truth is, however, as I pointed out recently that for all their hype, genome-wide association studies have produced meagre results. Your family medical history and lifestyle are much more likely to affect your health than the common variants genotyped in the current generation of microarrays. But, by all means, do your own research, since a trait that interests you may be one for which strong associations have been found.

Finally, the ancestral information is potentially useful, since recent papers have shown that multi-100K SNP genome-wide testing can produce fine-scale ancestral inference, even in relative homogeneous populations such as Europeans. However, as of this writing, you won't get this type of information, but rather a simple 4-group global admixture estimate, as well as a measure of your similarity to the Human Genome Diversity Panel populations. For anyone whose known genealogical ancestry isn't complex, this information will not be novel.

23andMe have also apparently included some fairly detailed SNP typing that place you in the Y-chromosome (if you are male) and mtDNA phylogeny, giving you a detailed haplogroup assessment. Even if this information wasn't known to me, this part of the test would not be tempting, since haplogroup assignment reveals only very coarse information. Almost certainly, you would want to follow up with a Y-STR panel or mtDNA full-genome sequence, which would allow you to meaningfully compare yourself with the many others that have tested so far; but that is not an option with 23andMe.

What is a 23andMe test worth to 23andMe?

23andMe have definitely emphasized the "coolness" factor of getting DNA tested. It has definitely generated a lot of publicity, and getting tested is marketed as a social prestige marker.

However, the "coolness" factor isn't enough to sell tests. It is not known how many have been sold so far, but there are indications that not many is close to the truth:

No one cuts the price by 60% if there is solid demand for a product. Prices for Y-STR tests haven't dropped by nearly as much in 5+ years, since there is a real demand for them by genetic genealogists.

People have a Gattaca-view of genetic testing, and are afraid of the information it may reveal. It has been said that 23andMe has downplayed the significance of the associations they report to keep regulators off their backs, but a more significant reason may be to entice reluctant consumers to test.

One would think that a company selling genetic tests would stress the importance of the genetic information, but this is clearly not the case. To its credit, 23andMe doesn't oversell the actual science, which as I mentioned above, isn't all that revealing.

Ms. Wojcicki and Linda Avey, the company’s other founder, say their chief goal is to advance science by compiling a database of genetic information that medical researchers can tap (while protecting customers’ anonymity). Customers cannot opt out of having their information anonymously shared, but they can refuse to participate in surveys focusing on specific traits.

This is also why the Coriell Institute is offering genotyping for free.

It is simply a problem of body count. Progress has been hampered by small sample sizes. Collecting and genotyping large samples is hampered both by strict ethics rules that publically-funded medical researchers must adhere to, and also by the actual cost of sample-collection and genotyping.

23andMe's goal isn't to be a service provider to consumers. Their goal is to entice regular people to pay the cost of genotyping, while at the same time helping it build its huge "database of genetic information."

Just as a TV station doesn't exist for providing news and entertainment to an audience, but provides news and entertainment so it can sell ads and make money, so 23andMe doesn't exist to sell genetic information to consumers, but sells genetic information to build and exploit its genetic database.

What it would take to make me a customer

There is nothing wrong with 23andMe's strategy: its goal is to advance science (and make money doing it) by offering genetic information to consumers. This is a potentially win-win situation for both. However, as I explained above, the information one can expect from the test today isn't all that special.

Since I don't want to be a naysayer, here is what it would take to convince me to test with 23andMe:

-- Fine-scale ancestry analysis --

The science has progressed to a point where this is possible. We now know that distinct subgroups can be discerned within all the major continental races. The latest research revealed an additional insight: it doesn't take a large samples to place individuals on the map fairly accurately. Even countries with less than 5 sampled individuals found their way to the "correct" geographical spot.

The corrolary of the above observation is that a global-level sampling of human genetic diversity can be done at a reasonable cost. Leveraging existing samples, and adding mini-samples from many unstudied locations can lead to powerful ancestry analysis, which can be gradually and continuously refined as more samples are collected (both on the "field" and using customers of unmixed localized heritage)

23andMe's partnership with ancestry.com suggests that they take this segment of their market seriously. So, when and if they offer a test which provides ancestral information beyond the obvious, I will be tempted to test with them.

5 comments:

"Customers cannot opt out of having their information anonymously shared"

I have a feeling that this will be a big hindrance for many people to use 23andMe (or services like it).

Who do you think will be the first one to provide a "kit" where people can do these kinds of genetics tests in their own homes (without having to go to any 3rd party)... with the ease one has for home pregnancy tests. And get the results right then and there, in a few minutes.

Who do you think will be the first one to provide a "kit" where people can do these kinds of genetics tests in their own homes (without having to go to any 3rd party)... with the ease one has for home pregnancy tests. And get the results right then and there, in a few minutes.

Excellent insights into 23andMe in this post. One implication is that the company might be interested in building the value of its own database by getting phenotypic and geneological information from its customers. To my knowledge, this is not the case.

It seems likely that the problems of matching genotype and phenotype are seen as currently insurmountable. If potential-customer skittishness about privacy already loom large, a series of probing questions could drive many away. Further, unvetted information could make such a database unreliable.

I tested with both 23andme and Decodeme. I just received my 23andme results and I am quite surprised by the admixture test named Ancestry Painting. Indeed I am half Berber, half French (E3b1b-M81, MtDna =I) but my 23andme results showed 100% European (African and Asian =0% ) whereas my DecodeMe results showed 81% European, 13% African ancestry and 6% Asian. So both results are very different. And I think it is not possible when somoeone has half berber ancestry to not show at least > 1 or 2 % of African/Asian ancestry. (Also I am sure they did not mix my sample with someone else as my Y-dna and mtDNA haplogroups are the same for both companies)

Do you know if these very different results can be because of different method used between 23andme and Decodeme ?

Decodeme seems to overestimate non-majority ancestry. It's possible that a North African Berber might have some Sub-Saharan ancestry, although this will depend on the individual case; Berbers are by no means homogeneous.

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